Skeletal myogenesis is characterized by the coordinated expression of a large number of genes. In skeletal muscle diseases and muscle tumors, many of these genes have an altered level of expression and emerging genomic technologies have been used to identify patterns of gene expression associated with normal differentiation and disease. Yet, the molecular basis for coordinately regulating subprograms of gene expression remains largely unknown. Our broad and long-term objective is to identify the molecular basis for the orchestrated regulation of subprograms of gene expression. Myogenesis provides an excellent model system, as it is known that the entire myogenic program can be initiated by a single transcription factor, MyoD. We have shown that MyoD directly patterns discrete subprograms of gene expression through a combination of regulated binding and promoter-specific activity. We will use our model of MyoD-induced myogenesis to test the broad hypothesis that complex patterns of gene expression are established by the regulated activity of a single transcription factor, rather than by multiple independent pathways. Our Specific Aims will (Aim 1) use a cell culture system of MyoD-mediated myogenesis to: (a) determine the molecular regulation of promoter-specific MyoD binding; (b) identify the promoter-specific role of individual activation domains of MyoD; and (c) determine the functionally relevant isoform of p38 and its mechanism of regulating MyoD; (Aim 2) use our in vitro system of MyoD-mediated transcription on chromatinized templates to directly test the roles of specific factors in sequential steps of transcriptional activation; and (Aim 3) use array analysis and the mouse and human genomic sequences to identify promoter motifs associated with specific subprograms of MyoD-mediated gene expression. The significance of this proposal is that we will reveal how a complex mixture of regulatory factors are integrated by a single transcription factor to orchestrate a coordinated pattern of gene expression. The health relatedness of this proposal is that the identification of the molecular basis of patterned gene expression will provide a fundamental framework for the study of gene expression in human development and disease.